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Item Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment(Springer Nature, 2024-08-27) Faraggi, Eshel; Jernigan, Robert L.; Kloczkowski, Andrzej; Physics, School of ScienceWe describe the machine learning tool that we applied in the CAGI 6 experiment to predict whether single residue mutations in proteins are deleterious or benign. This tool was trained using only single sequences, i.e., without multiple sequence alignments or structural information. Instead, we used global characterizations of the protein sequence. Training and testing data for human gene mutations was obtained from ClinVar (ncbi.nlm.nih.gov/pub/ClinVar/), and for non-human gene mutations from Uniprot (www.uniprot.org). Testing was done on post-training data from ClinVar. This testing yielded high AUC and Matthews correlation coefficient (MCC) for well trained examples but low generalizability. For genes with either sparse or unbalanced training data, the prediction accuracy is poor. The resulting prediction server is available online at http://www.mamiris.com/Shoni.cagi6.Item Parity-time-symmetric photonic topological insulator(Springer Nature, 2024) Fritzsche, Alexander; Biesenthal, Tobias; Maczewsky, Lukas J.; Becker, Karo; Ehrhardt, Max; Heinrich, Matthias; Thomale, Ronny; Joglekar, Yogesh N.; Szameit, Alexander; Physics, School of ScienceTopological insulators are a concept that originally stems from condensed matter physics. As a corollary to their hallmark protected edge transport, the conventional understanding of such systems holds that they are intrinsically closed, that is, that they are assumed to be entirely isolated from the surrounding world. Here, by demonstrating a parity-time-symmetric topological insulator, we show that topological transport exists beyond these constraints. Implemented on a photonic platform, our non-Hermitian topological system harnesses the complex interplay between a discrete coupling protocol and judiciously placed losses and, as such, inherently constitutes an open system. Nevertheless, even though energy conservation is violated, our system exhibits an entirely real eigenvalue spectrum as well as chiral edge transport. Along these lines, this work enables the study of the dynamical properties of topological matter in open systems without the instability arising from complex spectra. Thus, it may inspire the development of compact active devices that harness topological features on-demand.Item BPS equations and solutions for Maxwell–scalar theory(Elsevier, 2022) Morris, J. R.; Physics, School of ScienceEnergy minimizing BPS equations and solutions are obtained for a class of models in Maxwell–scalar theory, where an abelian electric charge is immersed in an effective dielectric of a real scalar field. The first order BPS equations are developed using the straightforward “on-shell method” introduced by Atmaja and Ramadhan. Employment of an auxiliary function of the scalar field allows a scalar potential that displays a tachyonic instability. Consequently, a nontopological scalar soliton is found to form around the charge. Examples and solutions are provided for (1) a point charge or sphere in a flat Minkowski background, and (2) an “overcharged” compact object in a Reissner–Nordstrom background. The solutions presented here for the former (Minkowski) case recover those that have been previously obtained, while the latter solutions are new BPS solutions.Item Polyhedral Distortions and Unusual Magnetic Order in Spinel FeMn2O4(American Chemical Society, 2023-03-14) Zhang, Qiang; Tian, Wei; Nepal, Roshan; Huq, Ashfia; Nagler, Stephen; DiTusa, J. F.; Jin, Rongying; Physics, School of ScienceSpinel compounds AB2X4 consist of both tetrahedral (AX4) and octahedral (BX6) environments with the former forming a diamond lattice and the latter a geometrically frustrated pyrochlore lattice. Exploring the fascinating physical properties and their correlations with structural features is critical in understanding these materials. FeMn2O4 has been reported to exhibit one structural transition and two successive magnetic transitions. Here, we report the polyhedral distortions and their correlations to the structural and two magnetic transitions in FeMn2O4 by employing the high-resolution neutron powder diffraction. The cation distribution is found to be (Mn0.92+Fe0.13+)A(Mn3+Fe0.93+Mn0.12+)BO4. While large trigonal distortion is found even in the high-temperature cubic phase, the first-order cubic-tetragonal structural transition associated with the elongation of both tetrahedra and octahedra with shared oxygen atoms along the c axis occurs at TS ≈ 750 K, driven by the Jahn-Teller effect of the orbital active B-site Mn3+ cation. Strong magnetoelastic coupling is unveiled at TN1 ≈ 400 K as manifested by the appearance of Néel-type collinear ferrimagnetic order, an anomaly in both tetrahedral and octahedral distortions, as well as an anomalous decrease of the lattice constants c and a weak anomaly of a. Upon cooling to TN2 ≈ 65 K, it evolves to a noncollinear ferrimagnetic order accompanied by the different moments at the split magnetic sites B1 and B2. Only one-half of the B-site Mn3+/Fe3+ spins, i.e., the B2-site spins in the pyrochlore lattice, are canted, which is a unique magnetic order among spinels. The canting angle between A-site and B2-site moments is ∼25°, but the B1-site moment stays antiparallel to the A-site moment even at 10 K. This noncollinear order is accompanied by a modification of the O-B-O bond angles in the octahedra without significant change in lattice constants or tetrahedral/octahedral distortion parameters, indicating a distinct magnetoelastic coupling. We demonstrate distinct roles of the A-site and B-site magnetic cations in the structural and magnetic properties of FeMn2O4. Our study indicates that FeMn2O4 is a wonderful platform to unveil interesting magnetic order and to investigate their correlations with polyhedral distortions and lattice.Item Location of dopamine in lipid bilayers and its relevance to neuromodulator function(Elsevier, 2023) Shafieenezhad, Azam; Mitra, Saheli; Wassall, Stephen R.; Tristram-Nagle, Stephanie; Nagle, John F.; Petrache, Horia I.; Physics, School of ScienceDopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.Item Net energy up-conversion processes in CdSe/CdS (core/shell) quantum dots, a possible pathway to towards optical cooling(American Physical Society, 2022) Hua, Muchuan; Decca, Ricardo S.; Physics, School of ScienceAn investigation of the possibility of optical refrigeration (OR) on zinc-blende cadmium selenide/cadmium sulfide (CdSe/CdS) core/shell structure quantum dots (QDs) has been carried out. Quality samples were synthesized in our laboratory, and significant energy up-conversion photoluminescence (UCPL) was observed in these samples, showing the potential of generating net cooling effects. To better understand and predict the UCPL characteristics of the QDs, a semiempirical model has been developed, showing good agreement with our experimental results. The model takes into account the corresponding quantum yield and cooling efficiency, predicting the possibility of realizing optical refrigeration on a CdSe QD system.Item Programmable high-dimensional Hamiltonian in a photonic waveguide array(Springer Nature, 2024-01-02) Yang, Yang; Chapman, Robert J.; Haylock, Ben; Lenzini, Francesco; Joglekar, Yogesh N.; Lobino, Mirko; Peruzzo, Alberto; Physics, School of ScienceWaveguide lattices offer a compact and stable platform for a range of applications, including quantum walks, condensed matter system simulation, and classical and quantum information processing. However, to date, waveguide lattice devices have been static and designed for specific applications. We present a programmable waveguide array in which the Hamiltonian terms can be individually electro-optically tuned to implement various Hamiltonian continuous-time evolutions on a single device. We used a single array with 11 waveguides in lithium niobate, controlled via 22 electrodes, to perform a range of experiments that realized the Su-Schriffer-Heeger model, the Aubrey-Andre model, and Anderson localization, which is equivalent to over 2500 static devices. Our architecture's micron-scale local electric fields overcome the cross-talk limitations of thermo-optic phase shifters in other platforms such as silicon, silicon-nitride, and silica. Electro-optic control allows for ultra-fast and more precise reconfigurability with lower power consumption, and with quantum input states, our platform can enable the study of multiple condensed matter quantum dynamics with a single device.Item Pre-processing of Galaxies in the Early Stages of Cluster Formation in Abell 1882 at z=0.139(American Astronomical Society, 2022) Sengupta, Aparajita; Keel, William C.; Morrison, Glenn; Windhorst, Rogier A.; Miller, Neal; Smith, Brent; Physics, School of ScienceA rare opportunity to distinguish between internal and environmental effects on galaxy evolution is afforded by “SuperGroups,” systems that are rich and massive, but include several comparably rich substructures, surrounded by filaments. We present here a multiwavelength photometric and spectroscopic study of the galaxy population in the SuperGroup Abell 1882 (A1882) at z = 0.139, combining new data from the MMT and Hectospec with archival results from the Galaxy And Mass Assembly survey, the Sloan Digital Sky Survey, the Nasa/IPAC Extragalactic Database, the Gemini Multi-Object Spectrograph, and the Galaxy Evolution Explorer. These provide spectroscopic classifications for 526 member galaxies, across wide ranges of local density and velocity dispersion. We identify three prominent filaments along which galaxies seem to be entering the SuperGroup (mostly in E–W directions). A1882 has a well-populated red sequence, containing most galaxies with stellar mass >1010.5 M Sun, and a pronounced color–density relation even within its substructures. Thus, galaxy evolution responds to the external environment as strongly in these unrelaxed systems as we find in rich and relaxed clusters. From these data, local density remains the primary factor, with a secondary role for distance from the inferred center of the entire structure’s potential well. The effects on star formation, as traced by optical and near-UV colors, depend on galaxy mass. We see changes in lower-mass galaxies (M < 1010.5 M Sun) at four times the virial radius of major substructures, while the more massive near-UV Green Valley galaxies show low levels of star formation within two virial radii. The suppression of star formation (“quenching”) occurs in the infall regions of these structures even before the galaxies enter the denser group environment.Item Visualization of human optic nerve by diffusion tensor mapping and degree of neuropathy(PLOS, 2022-12-12) Łabieniec, Łukasz; Lisowski, Łukasz; Petrache, Horia I.; Hładuński, Marcin; Konopińska, Joanna; Kochanowicz, Jan; Szymański , Krzysztof R.; Physics, School of ScienceDiffusion-weighted magnetic resonance imaging of the human optic nerve and tract is technically difficult because of its small size, the inherent strong signal generated by the surrounding fat and the cerebrospinal fluid, and due to eddy current-induced distortions and subject movement artifacts. The effects of the bone canal through which the optic nerve passes, and the proximity of blood vessels, muscles and tendons are generally unknown. Also, the limited technical capabilities of the scanners and the minimization of acquisition times result in poor quality diffusion-weighted images. It is challenging for current tractography methods to accurately track optic pathway fibers that correspond to known anatomy. Despite these technical limitations and low image resolution, here we show how to visualize the optic nerve and tract and quantify nerve atrophy. Our visualization method based on the analysis of the diffusion tensor shows marked differences between a healthy male subject and a male subject with progressive optic nerve neuropathy. These differences coincide with diffusion scalar metrics and are not visible on standard morphological images. A quantification of the degree of optic nerve atrophy in a systematic way is provided and it is tested on 9 subjects from the Human Connectome Project.Item Probing the screening of the Casimir interaction with optical tweezers(American Physical Society, 2021) Pires, L. B.; Ether, D. S.; Spreng, B.; Araújo, G. R. S.; Decca, R. S.; Dutra, R. S.; Borges, M.; Rosa, F. S. S.; Ingold, G.-L.; Moura, M. J. B.; Frases, S.; Pontes, B.; Nussenzveig, H. M.; Reynaud, S.; Viana, N. B.; Maia Neto, P. A.; Physics, School of ScienceWe measure the colloidal interaction between two silica microspheres in an aqueous solution in the distance range from 0.2 to 0.5 μm with the help of optical tweezers. When employing a sample with a low salt concentration, the resulting interaction is dominated by the repulsive double-layer interaction which is fully characterized. The double-layer interaction is suppressed when adding 0.22 M of salt to our sample, thus leading to a purely attractive Casimir signal. When analyzing the experimental data for the potential energy and force, we find good agreement with theoretical results based on the scattering approach. At the distance range probed experimentally, the interaction arises mainly from the unscreened transverse magnetic contribution in the zero-frequency limit, with nonzero Matsubara frequencies providing a negligible contribution. In contrast, such unscreened contribution is not included by the standard theoretical model of the Casimir interaction in electrolyte solutions, in which the zero-frequency term is treated separately as an electrostatic fluctuational effect. As a consequence, the resulting attraction is too weak in this standard model, by approximately one order of magnitude, to explain the experimental data. Overall, our experimental results shed light on the nature of the thermal zero-frequency contribution and indicate that the Casimir attraction across polar liquids has a longer range than previously predicted.